Iva Veseli of anvi'o

Bio

Computer scientist and biologist who leverages computational methods to study microbial metabolism in environmental metagenomes.

Affiliations

Contact info or affiliations needs an update? Edit these files.

Intellectual contributions

Some contributions are more than code. Inevitably, this manually curated list will be incomplete for almost everyone, but nevertheless, we try to keep track of key contributions made by memebers of the anvi'o commmunity to the platform and its users. Edit these files to help.

Program contributions

anvi-compute-functional-enrichment-across-genomes anvi-compute-functional-enrichment-in-pan anvi-compute-metabolic-enrichment anvi-display-metabolism anvi-estimate-metabolism anvi-migrate anvi-run-hmms anvi-run-kegg-kofams anvi-run-pfams anvi-setup-kegg-kofams anvi-setup-pfams anvi-setup-user-modules anvi-summarize-blitz anvi-script-gen-genomes-file anvi-script-gen-user-module-file

Resource contributions

Tutorials and exercises

Kinds of write-ups that typically use mock or simple datasets to describe basic concepts and how to accomplish common tasks in anvi'o often with hands-on experience.

An exercise on metabolic reconstruction A hands-on exercise for the metabolism suite of programs in anvi’o. It starts with a section on how to estimate metabolism for a single bacterial isolate, and goes into larger, real-world dataset of metagenome-assembled genomes to demonstrate how to estimate metabolism compute enrichment scores for metabolic modules.
metabolism metabolic enrichment genomics metagenomics hands-on beginner
A primer on anvi'o with the Infant Gut Dataset A tutorial that walks you through some of the most fundamental aspects of anvi'o and its application to a real-world dataset organized in multiple interconnected chapters, which all use the same dataset.
metagenomics binning pangenomics phylogenomics microbial population genetics hands-on beginner
A metagenomics workshop featuring anvi'o Materials from a 2022 workshop on metagenomics in anvi'o, including read recruitment and metabolism estimation.
metagenomics metabolism hands-on beginner

Technical write-ups

Solutions or discussions regarding matters that are typically more technical than scientific.

Getting help from the anvi'o community A resource that describes how to find anvi'o programs and understand their utility, how to reach out to anvi'o community, and how to report technical problems.
beginner

Articles, workflows, opinions

Key insights into specific topics and can be useful to more advanced users and 'omics enthusiasts in general.

Targeted binning of a novel nitrogen-fixing population from the Arctic Ocean Using metabolism estimation to go fishing in some ocean metagenomes.
metagenomics binning metabolism